Antimicrobial Usage Factors and Resistance Profiles of Shiga Toxin-Producing Escherichia coli in Backyard Production Systems From Central Chile

Abstract

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen and important cause of foodborne disease worldwide. Many animal species in backyard production systems (BPS) harbor STEC, systems characterized by low biosecurity and technification. No information is reported on STEC circulation, antimicrobial resistance (AMR) and potential drivers of antimicrobial usage in Chilean BPS, increasing the risk of maintenance and transmission of zoonotic pathogens and AMR generation. Thus, the aim of this study was to characterize phenotypic and genotypic AMR and to study the epidemiology of STEC isolated in BPS from Metropolitana region, Chile. A total of 85 BPS were sampled. Minimal inhibitory concentration and whole genome sequencing was assessed in 10 STEC strain isolated from BPS. All strains were cephalexin-resistant (100%, n = 10), and five strains were resistant to chloramphenicol (50%). The most frequent serotype was O113:H21 (40%), followed by O76:H19 (40%), O91:H14 (10%), and O130:H11 (10%). The stx1 type was detected in all isolated strains, while stx2 was only detected in two strains. The Stx subtype most frequently detected was stx1c (80%), followed by stx1a (20%), stx2b (10%), and stx2d (10%). All strains harbored chromosomal blaAmpC. Principal component analysis shows that BPS size, number of cattle, pet and horse, and elevation act as driver of antimicrobial usage. Logistic multivariable regression shows that recognition of diseases in animals (p = 0.038; OR = 9.382; 95% CI: 1.138–77.345), neighboring poultry and/or swine BPS (p = 0.006; OR = 10.564; 95% CI: 1.996–55.894), visit of Veterinary Officials (p = 0.010; OR = 76.178; 95% CI: 2.860–2029.315) and close contact between animal species in the BPS (p = 0.021; OR = 9.030; 95% CI: 1.385–58.888) increase significantly the risk of antimicrobial use in BPS. This is the first evidence of STEC strains circulating in BPS in Chile, exhibiting phenotypic AMR, representing a threat for animal and public health. Additionally, we identified factors acting as drivers for antimicrobial usage in BPS, highlighting the importance of integration of these populations into surveillance and education programs to tackle the potential development of antimicrobial resistance and therefore the risk for ecosystemic health.

Shiga toxin (stx) encoding genes in sheep and goats reared in Trinidad and Tobago

“…The preponderance of stx 1 isolates recovered from small ruminant animals has also been recorded in other epidemiological studies [11,15,[48][49][50]. This high proportion of stx 1 -positive isolates could be as a result of these isolates being better adapted to colonization of small ruminants than stx 2 or stx 1+2 -positive isolates.…”

“…Studies which have successfully identified O157 serogroup in sheep or goat feces report a prevalence of between 1.8-11.7% [25,[52][53][54][55]. Pavez-Munoz et al (2021) also failed to recover any O157 isolates from sheep samples collected as part of a backyard production system surveillance [49]. The absence or low prevalence of O157 STEC from sheep and goat feces indicates that sheep and goats may be an unlikely source of human O157 infection.…”

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

“…Twenty-one STEC strains isolated from cattle were sequenced in this study, of which twenty were isolated in 2018 from cattle at abattoirs in the Región Metropolitana of Chile [8], and one was isolated in 2019 from cattle raised in a backyard production system in the same region [49]. Genomic DNA of these 21 STEC strains was extracted using the Wizard Genomic DNA purification kit (Promega, Madison, WI, USA), following the manufacturer's instructions.…”

Risk Factors for Positivity to Shiga Toxin-Producing Escherichia coli and Salmonella enterica in Backyard Production Systems Animals from Metropolitana Region, Chile: A Threat to Public Health?

“…This fact may be an indirect indicator of a possible underestimation or overestimation of immunity levels for certain diseases [72,73]. The consequences of these practices could have an impact on public and animal health, mainly associated with the generation of antimicrobial resistance against widely used drugs [34,35,48,71,74,75]. Previous studies have detected multidrug resistance in non-typhoidal Salmonella strains from Chilean BPS [76] and sensitivity to a wide range of antimicrobials in STEC isolates from backyard animals [75].…”